Charm failing to properly segmentate MRIs #508
Replies: 2 comments 7 replies
-
|
Can you please check that the affine transformation looks good following the instructions here: Could you also check your MRI scans against the examples here: https://simnibs.github.io/simnibs/build/html/tutorial/head_meshing.html If they fall into the "bad" category, we can try to optimize the segmentation parameters that charm uses per default. |
Beta Was this translation helpful? Give feedback.
-
|
Sorry for the late reply! Yeah, the MRI scans are not the most optimal for charm, but what you can try is to run freesurfer as you suggested, and then run charm again like this: charm --fs-dir <fs_subject_dir> here the <fs_subject_dir> refers to the freesurfer output folder for the given subject. charm will then grab the surfaces from that folder and update the segmentation with those. That should help with the GM segmentation. |
Beta Was this translation helpful? Give feedback.

Uh oh!
There was an error while loading. Please reload this page.
-
Dear Simnibs team & community, we are currently preparing for an experiment in which we will be using Simnibs as a normalization tool for TMS intensities. However, charm has failed to produce good segmentation so far, as you can observe in the following examples coming from 2 different subjects. We have inspected the other layers and the white matter seems normal but the gray matter is not (as well as spongy bone maybe).
The affine registration seems normal.
For the segmentation we are using the charm command line with --forceqform , is there a way to improve the qualities? Many thanks in advance for your help!
Beta Was this translation helpful? Give feedback.
All reactions